The only real downside to I see to running pump 100% is extra wear, but as beagle says they're not too expensive. Higher flow rates will give you better cooling, and the power draw is probably insignificant.
I'm mounting mine near the passenger side corner, but I have a side feed intake manifold and the cooler has 90 degree outlets so it makes a really nice pathway.
You can always make heat shields to protect the cooler, and direct airflow. I'd worry about getting your intake path right, then worry about heat.